recipe r-beyondcell

Tool for the Analysis of tumour therapeutic heterogeneity in single-cell RNA-seq

Homepage:

https://gitlab.com/bu_cnio/beyondcell

License:

GPL-3

Recipe:

/r-beyondcell/meta.yaml

Beyondcell is a methodology for the identification of drug vulnerabilities in single-cell RNA-seq (scRNA-seq) data. To this end, Beyondcell focuses on the analysis of drug-related commonalities between cells by classifying them into distinct Therapeutic Clusters (TCs).

package r-beyondcell

versions:

1.3.3-1,  1.3.3-0

depends bioconductor-qusage:

>=2.22.0

depends numba:

0.46.*

depends python:

3.6.*

depends r-base:

>=4.2,<4.3.0a0

depends r-bnstruct:

>=1.0.6

depends r-cowplot:

>=1.1.0

depends r-deldir:

>=1.0_2

depends r-gdata:

>=2.18.0

depends r-ggplot2:

>=3.3.2

depends r-ggrepel:

>=0.8.2

depends r-patchwork:

>=1.0.1

depends r-plyr:

>=1.8.6

depends r-rcolorbrewer:

>=1.1-2

depends r-reshape2:

>=1.4.4

depends r-scales:

>=1.1.1

depends r-see:

depends r-seurat:

>=3.2.2

depends r-useful:

depends r-viridis:

>=0.5.1

depends umap-learn:

0.4.6.*

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install r-beyondcell

and update with::

   mamba update r-beyondcell

To create a new environment, run:

mamba create --name myenvname r-beyondcell

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/r-beyondcell:<tag>

(see `r-beyondcell/tags`_ for valid values for ``<tag>``)

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